Many of the most interesting and important neurobiological phenomena, as well as the pathological processes underlying neurological diseases, involve interactions at multiple levels. For example, certain forms of Alzheimer Disease result from mutations in the genes that code for the proteins that process the beta-amyloid peptide, the build-up of which results in the dysfunction and death of neurons, which in turn lead to failure of the neural circuits and brain regions that mediate memory and cognition. Other multilevel processes are implicated in other neurological and psychological disorders. Our work concerns the computational modeling of multilevel neurobiological process, with a current focus on Alzheimer and other neurodegenerative diseases, mood disorders including depression and anxiety, and eating disorders. By representing experimental findings formally as declarations in a computer program, the multilevel physiology and pathophysiology of various neurobiological processes can be explored through simulation and analysis, leading to experimentally testable predictions and new perspectives on possible pharmacological interventions.